MFB: Next-generation Proximity Labeling Technologies to Map Subcellular Transcriptomes and RNA Interactomes in Living Cells with Nanometer Resolution

In this Molecular Foundations for Biotechnology (MFB) project, Dr. Alice Ting and her team at Stanford University will embark on an effort to develop new technologies for studying RNA, the essential molecules that carry genetic information, encode proteins, and play crucial roles in cell functions. Traditionally, our understanding of RNA has been limited by methods that require breaking cells apart, leading to information loss. The team's goal is to create non-destructive technologies that allow scientists to directly study RNA in living cells, offering new insights into their location, interactions, and functions. This research is particularly significant for human health, as disruptions in RNA are implicated in many diseases, including cancer. The project extends beyond its scientific impact by fostering collaborations, conducting workshops, and engaging in outreach activities to introduce under-represented students to the exciting world of RNA science. This project addresses current limitations in studying RNA within living cells by leveraging proven proximity labeling (PL) technologies previously used for proteins. Drawing on over a decade of PL experience, the research team aims to: (1) develop new methods for transcriptome-wide mapping of RNA localization in living cells, achieving single-cell resolution with improved labeling chemistries; (2) create RNA-centric interactome mapping tools through protein engineering and directed evolution; and (3) apply these technologies to cancer biology, collaborating with experts to explore tumor-immune cell interactions and map specific cancer-associated RNA interactomes. The project's intellectual merit stems from the team's multidisciplinary expertise, spanning protein and RNA engineering, directed evolution, chemical biology, computational analysis, and cancer biology. Broader impacts include the creation of widely applicable tools, educational opportunities, and potential advancements in cancer therapeutics, contributing to improvements in public health. This project is supported by the Division of Chemistry in the Directorate for Mathematical and Physical Sciences, and by the Division of Molecular and Cellular Biosciences and Systems and Synthetic Biology cluster in the Directorate for Biological Sciences. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.